it looks like your design is emphasizing the stone entrance area, so i would make that pop, and let everything else play a supporting role. i definitely recommend making the front door larger, either a taller door, or wider sidelights, plus definitely adding a transom across the top for height. use a more Craftsman style door rather than the 6-panel Colonial shown. the stone bases of the columns might look better if the tops were closer to the porch floor level, and the stone bases extended into the ground. in emphasizing the entry, i don't see the need for board and batten on the porch (calls attention away from the entrance).
colors - red cedar timber frame will naturally weather to a soft gray, so i would continue with shades of lighter and darker gray on the shingles, stone, and siding (and matching garage door to blend in). there is an opportunity for color on the trimwork, with a neutral front door (dark wood brown or glossy black). or vice versa, with neutral white, off-white, or bronze trim, and a punch of color for the door. the hefty columns look best natural - or painted dark brown or black.
in keeping with the heavy Craftsman or rustic inspired architecture, colors i would consider are forest green, dark berry purple, and cranberry red, those you'd find in nature. the stonework could then have a smattering of stones in grays, light greens, and light purply-reds.